Abstract

RNA interference (RNAi) is a conserved mechanism for post-transcriptional gene regulation and a critical process of arthropod immunity. This study investigates RNAi-associated genes in Caligus rogercresseyi, an ectoparasitic sea louse that poses significant challenges to salmon aquaculture. In that regard, 16 RNAi-associated genes were identified by in silico analysis, including Cr-AGO1, Cr-CNOT1, Cr-DCR, Cr-SND1, and Cr-XRN1. Phylogenetic analysis demonstrated clustering with homologous sequences from other arthropods, particularly the ectoparasitic copepod Lepeophtheirus salmonis. RNA-Seq analyses revealed developmentally regulated expression patterns, with RNAi-associated genes clustered into four distinct expression profiles. Quantitative PCR (qPCR) validation confirmed significant male-biased expression for several key genes, including Cr-AGO1 (109-fold increase), Cr-DCR (22-fold), Cr-XRN1 (22-fold), Cr-SND1 (fourfold), and Cr-CNOT1 (threefold), suggesting potential roles in male reproductive processes such as spermatogenesis. Cr-DDX6, Cr-Drosha, and Cr-XPO5, potentially involved in oocyte development and RNA transport, exhibited female-biased expression. These results provide new insights into RNAi-associated gene expression in C. rogercresseyi, uncovering significant developmental and sex-biased expression patterns. Characterizing these critical genes establishes a foundation for exploring control strategies based on the RNAi process, targeting sex-biased and developmentally essential genes. Such treatments could reduce reproductive success in sea lice while minimizing environmental impact, offering a sustainable alternative for managing caligidosis in aquaculture. © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2025.